The Upper Dock extends to 2 ha (5 acres) and comprises Trinity Quay, Upper Quay and Jamieson's Quay, including the NorthLink ferry terminal. Once separated from the Upper Dock by the Regent Opening Bridge (demolished 1974), the 11.3-ha (28-acre) Victoria Dock comprises Blaikie's Quay to the south and the deep-water berths of Regent Quay and Waterloo Quay to the north. Blaikie's Quay and Jamieson's Quay were both named after Provosts of Aberdeen, who served during the mid-19th century when the most important harbour improvements took place. Waterloo Quay is the only part of the harbour still accessible by rail, and was once the site of Waterloo Station, the southern terminus of the Great North of Scotland Railway between 1856 and 1867. The railway was built along the route of the Aberdeenshire Canal which opened in 1805 but was never a great financial success.
Victoria Dock and the Upper Dock were once isolated from the outer tidal section of the harbour by locks, but these were removed in 1975 and replaced by Matthews' Quay, with its roll-on-roll-off ramp, as part of improvements made for the oil industry. Matthews' Quay was named after James Matthews (1819-98) another Lord Provost who was also a noted architect in the city. Telford Dock combines deep-water berths with a ship-repair area, built on the site of the former Hall Russell shipyard which closed in 1992, and now comprises Duthie's Quay, Clipper Quay, Hall's Quay and Russell's Quay and includes a lifeboat station and dry-dock.
The 8.5-ha (21-acre) Albert Basin was constructed within the former channel of the Dee, the river having been controlled allowing the reclamation of a considerable area of land. This basin provides the majority of deep-water berths including the 137-m (450-foot) long Atlantic Wharf, the 250-m (672-foot) long Pacific Wharf (both constructed in the 1950s), Albert Quay and Commercial Quay. Palmerston Quay at the western end of the Albert Basin handles fishing boats, and includes an ice factory and fish-market, much reduced in size in recent years. The Telford Dock and Albert Basin open into a wider area of water known as the Tidal Harbour, which extends to 14.5 ha (36 acres) and includes the Pocra Quay on its eastern side, next to Footdee, together with the jetty used by the harbour pilots.
The berths along the River Dee are shallow but extend to 928m (3044 feet) and include a marine safety training centre, the Mearns Quay, Torry Quay and, within the River Dee Dock, Maitland's Quay.
The harbour also includes numerous transit and cargo-handling sheds.